Gillibrand criticized Rooney for her testimony at her confirmation hearing earlier this month, where Rooney argued in opposition to Gillibrand’s proposal that would take sexual assault cases away from military commanders.

“A judge advocate outside the chain of command will be looking at a case through a different lens than a military commander,” Gillibrand read from Rooney’s statement at the hearing.

“I believe the impact would be decisions based on evidence, rather than the interest in preserving good order and discipline. I believe this will result in fewer prosecutions and therefore defeat the problem that I understand it seeks to address,” Rooney wrote.

In a statement Thursday, Gillibrand said that statements like Rooney’s “further erode” the trust that justice can be served in the military system.

“If you were a service member raped on duty, why would you have confidence to come forward and report after hearing that basing decisions to prosecute solely on evidence would be a bad outcome?” Gillibrand said. “Jo Ann Rooney’s testimony should send chills down the spine of any member of the armed services seeking justice.”

At the hearing, Rooney said that she did not mean to suggest a commander would ignore evidence, but said that a commander has additional issues to consider within his or her command.

The issue strikes at the heart of Gillibrand’s push in Congress to remove the decision to prosecute cases from the military’s chain of command, a proposal opposed by top military leaders.

Gillibrand is seeking to get her measure included as an amendment to the Defense authorization bill, which will be on the Senate floor this month. Her office says 46 senators have backed it.

Pentagon officials, as well as Senate Armed Services Committee Chairman Carl Levin (D-Mich.), are against it, arguing that commanders need to retain the responsibility so they can be held accountable.

A Navy spokeswoman declined to comment on the hold because the nomination was pending.

Rooney’s nomination isn’t the first to be held up this year as a result of issues surrounding military sexual assault.

McCaskill said she has placed a hold on Helms because of an overturned guilty verdict in a case last year.

“With her action, Lt. Gen. Helms sent a damaging message to survivors of sexual assault who are seeking justice in the military justice system,” McCaskill said in June.

The issue of overturned guilty verdicts sparked widespread outrage in the Senate after an Air Force case this year, which led to Defense Secretary Chuck Hagel proposing an end to commanders’ ability to completely overturn verdicts in a post-trial review.

The proposal has been included in both the House and Senate Defense authorization bills.